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- EMDB-0268: Complex IV in the III2-IV2 mitochondrial respiratory supercomplex... -

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Basic information

Entry
Database: EMDB / ID: EMD-0268
TitleComplex IV in the III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae (CIVb)
Map dataThe second complex IV of the III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae
Sample
  • Complex: 12-subunit cytochrome c oxidase with isoform Cox5A
    • Protein or peptide: x 12 types
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsHartley AM / Lukoyanova N / Pinotsis N / Marechal A
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/M00936X/1 United Kingdom
Wellcome Trust105628/Z/14/Z United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: Structure of yeast cytochrome c oxidase in a supercomplex with cytochrome bc.
Authors: Andrew M Hartley / Natalya Lukoyanova / Yunyi Zhang / Alfredo Cabrera-Orefice / Susanne Arnold / Brigitte Meunier / Nikos Pinotsis / Amandine Maréchal /
Abstract: Cytochrome c oxidase (complex IV, CIV) is known in mammals to exist independently or in association with other respiratory proteins to form supercomplexes (SCs). In Saccharomyces cerevisiae, CIV is ...Cytochrome c oxidase (complex IV, CIV) is known in mammals to exist independently or in association with other respiratory proteins to form supercomplexes (SCs). In Saccharomyces cerevisiae, CIV is found solely in an SC with cytochrome bc (complex III, CIII). Here, we present the cryogenic electron microscopy (cryo-EM) structure of S. cerevisiae CIV in a IIIIV SC at 3.3 Å resolution. While overall similarity to mammalian homologs is high, we found notable differences in the supernumerary subunits Cox26 and Cox13; the latter exhibits a unique arrangement that precludes CIV dimerization as seen in bovine. A conformational shift in the matrix domain of Cox5A-involved in allosteric inhibition by ATP-may arise from its association with CIII. The CIII-CIV arrangement highlights a conserved interaction interface of CIII, albeit one occupied by complex I in mammalian respirasomes. We discuss our findings in the context of the potential impact of SC formation on CIV regulation.
History
DepositionOct 3, 2018-
Header (metadata) releaseOct 10, 2018-
Map releaseDec 26, 2018-
UpdateOct 9, 2019-
Current statusOct 9, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0268.png

Downloads & links

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Map

FileDownload / File: emd_0268.map.gz / Format: CCP4 / Size: 113.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe second complex IV of the III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 310 pix.
= 429.691 Å		1.39 Å/pix.
x 310 pix.
= 429.691 Å		1.39 Å/pix.
x 310 pix.
= 429.691 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3861 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.011 / Movie #1: 0.03
Minimum - Maximum-0.1074029 - 0.19403128
Average (Standard dev.)0.00014159399 (±0.004339733)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions310310310
Spacing310310310
CellA=B=C: 429.691 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.38611.38611.3861
M x/y/z310310310
origin x/y/z0.0000.0000.000
length x/y/z429.691429.691429.691
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS310310310
D min/max/mean-0.1070.1940.000

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Supplemental data

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Sample components

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Entire : 12-subunit cytochrome c oxidase with isoform Cox5A

EntireName: 12-subunit cytochrome c oxidase with isoform Cox5A
Components
  • Complex: 12-subunit cytochrome c oxidase with isoform Cox5A
    • Protein or peptide: Cox1
    • Protein or peptide: Cox2
    • Protein or peptide: Cox3
    • Protein or peptide: Cox4
    • Protein or peptide: Cox5A
    • Protein or peptide: Cox6
    • Protein or peptide: Cox7
    • Protein or peptide: Cox8
    • Protein or peptide: Cox9
    • Protein or peptide: Cox12
    • Protein or peptide: Cox13
    • Protein or peptide: Cox26

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Supramolecule #1: 12-subunit cytochrome c oxidase with isoform Cox5A

SupramoleculeName: 12-subunit cytochrome c oxidase with isoform Cox5A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303-1B

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Macromolecule #1: Cox1

MacromoleculeName: Cox1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MVQRWLYSTN AKDIAVLYFM LAIFSGMAGT AMSLIIRLEL AAPGSQYLHG NSQLFNVLVV GHAVLMIFF LVMPALIGGF GNYLLPLMIG ATDTAFPRIN NIAFWVLPMG LVCLVTSTLV E SGAGTGWT VYPPLSSIQA HSGPSVDLAI FALHLTSISS LLGAINFIVT ...String:
MVQRWLYSTN AKDIAVLYFM LAIFSGMAGT AMSLIIRLEL AAPGSQYLHG NSQLFNVLVV GHAVLMIFF LVMPALIGGF GNYLLPLMIG ATDTAFPRIN NIAFWVLPMG LVCLVTSTLV E SGAGTGWT VYPPLSSIQA HSGPSVDLAI FALHLTSISS LLGAINFIVT TLNMRTNGMT MH KLPLFVW SIFITAFLLL LSLPVLSAGI TMLLLDRNFN TSFFEVSGGG DPILYEHLFW FFG HPEVYI LIIPGFGIIS HVVSTYSKKP VFGEISMVYA MASIGLLGFL VWSHHMYIVG LDAD TRAYF TSATMIIAIP TGIKIFSWLA TIHGGSIRLA TPMLYAIAFL FLFTMGGLTG VALAN ASLD VAFHDTYYVV GHFHYVLSMG AIFSLFAGYY YWSPQILGLN YNEKLAQIQF WLIFIG ANV IFFPMHFLGI NGMPRRIPDY PDAFAGWNYV ASIGSFIATL SLFLFIYILY DQLVNGL NN KVNNKSVIYN KAPDFVESNT IFNLNTVKSS SIEFLLTSPP AVHSFNTPAV QS

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Macromolecule #2: Cox2

MacromoleculeName: Cox2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
SequenceString: DVPTPYACYF QDSATPNQEG ILELHDNIMF YLLVILGLVS WMLYT IVMT YSKNPIAYKY IKHGQTIEVI WTIFPAVILL IIAFPSFILL YLCDEVISPA MTIKAI GYQ WYWKYEYSDF INDSGETVEF ESYVIPDELL EEGQLRLLDT DTSMVVPVDT HIRFVVT AA ...String:
DVPTPYACYF QDSATPNQEG ILELHDNIMF YLLVILGLVS WMLYT IVMT YSKNPIAYKY IKHGQTIEVI WTIFPAVILL IIAFPSFILL YLCDEVISPA MTIKAI GYQ WYWKYEYSDF INDSGETVEF ESYVIPDELL EEGQLRLLDT DTSMVVPVDT HIRFVVT AA DVIHDFAIPS LGIKVDATPG RLNQVSALIQ REGVFYGACS ELCGTGHANM PIKIEAVS L PKFLEWLNEQ

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Macromolecule #3: Cox3

MacromoleculeName: Cox3 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
SequenceString: MTHLERSRHQ QHPFHMVMPS PWPIVVSFAL LSLALSTALT MHGYIGNMNM VYLALFVLLT SSILWFRDI VAEATYLGDH TMAVRKGINL GFLMFVLSEV LIFAGLFWAY FHSAMSPDVT L GACWPPVG IEAVQPTELP LLNTIILLSS GATVTYSHHA LIAGNRNKAL ...String:
MTHLERSRHQ QHPFHMVMPS PWPIVVSFAL LSLALSTALT MHGYIGNMNM VYLALFVLLT SSILWFRDI VAEATYLGDH TMAVRKGINL GFLMFVLSEV LIFAGLFWAY FHSAMSPDVT L GACWPPVG IEAVQPTELP LLNTIILLSS GATVTYSHHA LIAGNRNKAL SGLLITFWLI VI FVTCQYI EYTNAAFTIS DGVYGSVFYA GTGLHFLHMV MLAAMLGVNY WRMRNYHLTA GHH VGYETT IIYTHVLDVI WLFLYVVFYW WGV

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Macromolecule #4: Cox4

MacromoleculeName: Cox4 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
SequenceString:
QQKPVVKTAQ NLAEVNGPET LIGPGAKEGT VPTDL DQET GLARLELLGK LEGIDVFDTK PLDSSRKGTM KDPIIIESYD DYRYVGCTGS PAGSHT IMW LKPTVNEVAR CWECGSVYKL NPVGVPNDDH HH

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Macromolecule #5: Cox5A

MacromoleculeName: Cox5A / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
SequenceString:
QTHALSNAAV MDLQSRWENM PSTEQQDIVS KLSERQKLP WAQLTEPEKQ AVWYISYGEW GPRRPVLNKG DSSFIAKGVA AGLLFSVGLF AVVRMAGGQD AKTMNKEWQ LKSDEYLKSK NANPWGGYSQ VQSK

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Macromolecule #6: Cox6

MacromoleculeName: Cox6 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
SequenceString:
SDAHDEETFE EFTARYEKEF DEAYDLFEV QRVLNNCFSY DLVPAPAVIE KALRAARRVN DLPTAIRVFE ALKYKVENED Q YKAYLDEL KDVRQELGVP LKEELFPSSS

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Macromolecule #7: Cox7

MacromoleculeName: Cox7 / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
SequenceString:
ANKVIQLQKI FQSSTKPLWW RHPRSALYLY PFYAIFAVAV VTPLLYIPNA IRGIKAKKA

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Macromolecule #8: Cox8

MacromoleculeName: Cox8 / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
SequenceString:
VHFKDGVYEN IPFKVKGRKT PYALSHFGFF AIG FAVPFV ACYVQLKK

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Macromolecule #9: Cox9

MacromoleculeName: Cox9 / type: protein_or_peptide / ID: 9 / Enantiomer: LEVO
SequenceString:
TIAPITGTIK RRVIMDIVLG FSLGGVMASY WWWGFHMDKI NKREKFYAEL AERKK

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Macromolecule #10: Cox12

MacromoleculeName: Cox12 / type: protein_or_peptide / ID: 10 / Enantiomer: LEVO
SequenceString:
ADQENSPLHT VGFDARFPQQ NQTKHCWQSY VDYHKCVNMK GEDFAPCKVF WKTYNALCP LDWIEKWDDQ REKGIFAGDI NSD

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Macromolecule #11: Cox13

MacromoleculeName: Cox13 / type: protein_or_peptide / ID: 11 / Enantiomer: LEVO
SequenceString:
ASSLPPNALK PAFGPPDKVA AQKFKESLMA TEKHAKDTSN MWVKISVWVA L PAIALTAV NTYFVEKEHA EHREHLKHVP DSEWPRDYEF MNIRSKPFFW GDGDKTLFWN PV VNRHIEH DD

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Macromolecule #13: Cox26

MacromoleculeName: Cox26 / type: protein_or_peptide / ID: 13 / Enantiomer: LEVO
SequenceString:
MFFSQVLRSS ARAAPIKRYT GGRIGESWVI TEGRRLIPEI FQWSAVLSVC LGWPGAVYFF SKARKA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE / Chamber humidity: 92 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: 3 uL of sample applied to negatively glow discharged grid, blot force -10; blotting time 8.5 sec.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Sampling interval: 5.0 µm / Average exposure time: 8.0 sec. / Average electron dose: 1.645 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 44915
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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